rnaseq-de/main
View on GitHub
Download RO-Crate
Run on GalaxyIdentifies differentially expressed genes between exactly two experimental conditions from count tables. The workflow performs statistical testing, applies filters based on adjusted p-value and log2 fold change thresholds, and generates publication-quality visualizations including volcano plots, MA plots, and heatmaps. Takes two collections of count tables as input and produces filtered gene lists and interactive plots for interpreting expression differences. Optimal for simple two-condition experimental designs.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Adjusted p-value threshold | Adjusted p-value threshold | Adjusted p-value threshold to call genes as differentially expressed in diagnostic plots. If not set, default 0.05 is used. |
|
| Count files have header | Count files have header | Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have. |
|
| Counts from changed condition | Counts from changed condition | Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples. |
|
| Counts from reference condition | Counts from reference condition | Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples. |
|
| Gene Annotaton | Gene Annotaton | The same annotation GTF used for mapping and counting |
|
| log2 fold change threshold | log2 fold change threshold | log2 fold change threshold to filter for highly regulated genes. If not set, default 1.0 is used. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3 |
| 7 | Differential Analysis | toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy2 |
| 8 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 9 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3 |
| 10 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 11 | Annotate DESeq2/DEXSeq output tables | toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0+galaxy1 |
| 12 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 13 | Annotate DESeq2 table | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 |
| 14 | Parse parameter value | param_value_from_file |
| 15 | Filter with p-adj threshold | Filter1 |
| 16 | Generate Volcanot plot of DE genes | toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/4.0.1+galaxy0 |
| 17 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 18 | Filter with log2 FC threshold | Filter1 |
| 19 | Join two Datasets | join1 |
| 20 | Cut | Cut1 |
| 21 | Generate Heatmap of counts | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.3.0+galaxy0 |
| 22 | Generate Heatmap of Z-scores | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.3.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| DESeq2 Plots | DESeq2 Plots | n/a |
|
| DESeq2 Normalized Counts | DESeq2 Normalized Counts | n/a |
|
| Annotated DESeq2 results table | Annotated DESeq2 results table | n/a |
|
| Volcano Plot of DE genes | Volcano Plot of DE genes | n/a |
|
| Significantly differentially expressed genes | Significantly differentially expressed genes | n/a |
|
| Heatmap of log transformed normalized counts | Heatmap of log transformed normalized counts | n/a |
|
| Heatmap of Z-scores | Heatmap of Z-scores | n/a |
|
Version History
v0.1 (earliest) Created 13th Nov 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1d0491c7
Creators and SubmitterViews: 5335 Downloads: 33856 Runs: 1
Created: 13th Nov 2024 at 03:02
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
https://orcid.org/0000-0002-5192-126X
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
